3VRLC

Crystal structure of bmj4 p24 capsid protein in complex with a10f9 fab
Total Genus 23
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The genus trace: a function that shows values of genus (vertical axis) for subchains spanned between the first residue, and all other residues (shown on horizontal axis). The number of the latter residue and the genus of a given subchain are shown interactively.

Total Genus
23
sequence length
73
structure length
73
Chain Sequence
SILDIKQGPKESFRDYVDRFFKTLRAEQCTQDVKNWMTDTLLVQNANPDCKTILRALGPGATLEEMMTACQGV
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The genus matrix. At position (x,y) a genus value for a subchain spanned between x’th and y’th residue is shown. Values of the genus are represented by color, according to the scale given on the right.

Structure visualization

After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.

Chord Diagram
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publication title Structure of the HIV-1 capsid protein p24 in complex with the broad-spectrum antibody A10F9
rcsb
source organism Human immunodeficiency virus 1
molecule tags Immune system/viral protein
molecule keywords A10F9 Fab heavy chain
total genus 23
structure length 73
sequence length 73
chains with identical sequence D
ec nomenclature
pdb deposition date 2012-04-12

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
C PF00607 Gag_p24 gag gene protein p24 (core nucleocapsid protein)
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
1.10.1200.30 Mainly Alpha Orthogonal Bundle Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A 3vrlC00
5DCKA 4WYMA 4U0EA 2M8LA 4U0AA 3G0VA 3H47A 3DS0A 4PH1A 4COPA 5HGOA 5I4TG 4U0CA 2L6EA 1A43A 1E6JP 4U0FA 5HGMA 4XROA 3DS1A 1D1DA 2M8NA 3G21A 3LRYA 1EOQA 4COCA 1BAJA 4XFZA 3G28A 2M8PA 2KODA 2JYGA 2XXMA 2XT1A 1A8OA 4XFXA 2JO0A 3DPHA 5HGNA 3H4EA 4U0DA 3VRLC 4PH0A 2EIAA 3MGEA 3NTEA 4IPYA 1EIAA 5HGLA 2ONTA 4QNBA 2JYLA 3DS3A 3G1IA 3P05A 2XV6A 3DS2A 4XRQA 1QRJA 4XFYA 5JPAA 3DS4A 3DS5A 3G26A 3DTJA 3G29A 4U0BA 2LF4A 4M0IA 1AUMA 2BUOA 3G1GA
chains in the Genus database with same CATH superfamily
2JBGA 2M8LA 3H47A 3CCMP 4COPA 3CMAP 2CQ8A 2KR5A 1AF8A 4BPHA 1VQ8P 2KWLA 2VLPA 3CC2P 2FVEA 2OTJP 2OARA 2FAEA 3CMEP 3EJEA 3G26A 2MR7A 2LF4A 2N98A 3CE7A 2LOLA 1AYIA 4XROA 1D1DA 2FHSC 5HVCA 2KOQA 2QEXP 2KGEA 3G71P 2K2QA 1YI2P 1QVGO 1GPJA 3HZQA 2E1MA 2LTEA 5JPAA 2LMLA 1GXHA 4BPGA 3RG2A 1VQ7P 2GZIA 4R0MA 1S72P 1VHNA 5KP7B 2PEKA 1KC8Q 1L0IA 2KGCA 3P05A 3DS2A 2QA4P 1RNIA 3EJDA 2AFDA 3CXCO 2L6EA 2KG9A 2L0QA 2OTLP 1VQ4P 1NQ4A 2K5XA 2GZGA 2N50A 2VSQA 4U0DA 2FADA 1K8AQ 2JGPA 1ACPA 2XZ1C 4GR6A 1E0HA 1HQBA 2XV6A 2KORA 2PEIA 2K94A 2GDYA 1YIJP 2L4BA 1K73Q 2MR8A 1KLPA 2M8NA 3G6EP 1BAJA 3CC4P 1F80D 2JB0A 3CPWO 3CCSP 2PEOA 1BXIA 2KW2A 4GR2A 4CA3A 1DV5A 2MY5A 1VQNP 2DGYA 1YJWP 5HV8A 1KQSO 1M6NA 3B4QA 5HGMA 3CCVP 2K92A 2M8PA 2CWOA 3I55P 4XFXA 2ROQA 4PH0A 3VRLC 2EIAA 2KG6A 2JYLA 2MF4A 4H2XC 3I56P 3G1GA 2KOOA 4U0AA 1NJIQ 2N6YA 5BS1A 5HGOA 3CCUP 3CCEP 1VQOP 2XZ0D 3NY7B 1M74A 2XXMA 2Z46A 1A8OA 2JO0A 2JU1A 3Q20A 1DNYA 2ONTA 2LPKA 1EMVA 2AFEA 2NO8A 3G0VA 2K0XA 2N5HA 3GZLA 3CC7P 4UHPB 4HKGA 2FQ1A 5EJDA 2AVAA 3DPHA 2K0YA 2MVUA 2L9FA 4XFYA 1QVFO 2JAZA 2BUOA 3CCLP 5BS2A 3CCJP 2JU2A 3OW2O 4XFZA 3G28A 2LL8A 2Z45A 2GZEA 2KG8A 3HYBA 1KD1Q 4QNBA 3U43A 5KP8B 2GYKA 5F2KA 5DCKA 2K0DX 1ZMBA 3DS0A 2KGAA 4U0FA 1E6JP 1Q82Q 1K30A 1VKUA 1VQLP 4IPYA 3CCRP 3M1MA 2LIUA 2K93A 2KOPA 2PNGA 4U0EA 1VQ6P 1YJNP 1A43A 1Q81Q 3RG6C 3CCQP 3LMOA 1ZNVA 2EHTA 4H2YC 3NTEA 1EIAA 1RO2A 1T8KA 3GJNA 1RO0A 2N6ZA 2GZFA 1UJZA 4PH1A 5F2NA 5I4TG 2LIWA 3GZMA 2N5IA 3G21A 1HY8A 1CEIA 2JYGA 2XT1A 2GDXA 1FR2A 2ERHA 1QRJA 4NEOA 1VQ5P 1GXGA 1L0HA 2FVAA 2L22A 3GKLC 4U0CA 3LRYA 4IZ6A 1EOQA 3EJBA 2KODA 1OR5A 2FACA 2EHSA 3H4EA 3CD6P 2BHVA 3MGEA 5KP6B 1N8RQ 4XRQA 1M1KQ 7CEIA 2M5RA 3DS4A 5F2OA 4QKOA 4WYMA 2PENA 2PY8A 3G4SP 1JJ2O 2EFJA 1YHQP 1W2BO 2AF8A 2CG5B 1IMQA 2PEJA 5EW5E 1YITP 5CZDB 4MRTC 1IUQA 1MZ8A 1M6EX 5HGLA 2FQ2A 2Z44A 1Q86Q 4U0BA 1Q7YQ 4BPFA 2KGDA 2PEMA 2P9XA 2GZJA 3WBHA 1VQ9P 3DS1A 2LKIA 4COCA 4DG9A 4F37A 1VQKP 2VLNA 2EG5A 2GDWA 1VQMP 1M90Q 5HGNA 2FQ0A 1UNKA 3DS3A 4PWVB 3G1IA 4PXHB 1VQPP 1YJ9P 4M0IA 3E2DA 2CNRA 2MD9A 3B5IA 3H0DA 2PEQA 1IMPA 2KOSA 2WPTA 1K9MQ 1X3OA 4H2WC 2DNWA 2MVVA 2QNWA 2VLOA 2X2BA 2CGQA 2FVFA 1Z6MA 3DS5A 3DTJA 3G29A 2VLQA 1AUMA 2JQ4A
chains in the Genus database with same CATH topology
2PEIA 2M8LA 1VQ5P 3H47A 3CCMP 4COPA 1YIJP 4U0CA 3CMAP 3CCLP 5BS2A 1K73Q 3CCJP 3OW2O 2M8NA 3G6EP 3LRYA 1EOQA 1BAJA 4XFZA 3CC4P 3G28A 1VQ8P 2KODA 3CPWO 2Z45A 3CCSP 3CC2P 2OTJP 3H4EA 3HYBA 3CD6P 2BHVA 2PEOA 3MGEA 1KD1Q 2OARA 4QNBA 1N8RQ 3CMEP 4XRQA 1M1KQ 4GR2A 3DS4A 3G26A 5F2OA 2LF4A 5F2KA 1VQNP 5DCKA 4WYMA 2DGYA 1ZMBA 2PENA 2PY8A 3DS0A 3G4SP 1JJ2O 2EFJA 1YHQP 1YJWP 1W2BO 1KQSO 1M6NA 5HGMA 4U0FA 1E6JP 4XROA 2PEJA 3CCVP 1YITP 1D1DA 1Q82Q 2M8PA 1K30A 1IUQA 2QEXP 2CWOA 1M6EX 3I55P 4XFXA 3G71P 4PH0A 3VRLC 1VQLP 1YI2P 2EIAA 4IPYA 5HGLA 1QVGO 3HZQA 3CCRP 3M1MA 2JYLA 2E1MA 2Z44A 1Q86Q 5JPAA 4U0BA 3I56P 1Q7YQ 3G1GA 2PEMA 4U0EA 4U0AA 1VQ6P 2P9XA 1NJIQ 5HGOA 5BS1A 3WBHA 3CCUP 1YJNP 3CCEP 1A43A 1VQOP 1VQ7P 1VQ9P 3DS1A 1Q81Q 3RG6C 4COCA 1S72P 3CCQP 1VQKP 2EG5A 1M74A 1VQMP 2XXMA 2Z46A 1M90Q 2PEKA 1A8OA 2JO0A 1KC8Q 5HGNA 3Q20A 3NTEA 1EIAA 2ONTA 3DS3A 3G1IA 1RO2A 3P05A 3DS2A 1VQPP 1YJ9P 2QA4P 1RNIA 4M0IA 1RO0A 3E2DA 3G0VA 4PH1A 3B5IA 5F2NA 3H0DA 2PEQA 5I4TG 3CXCO 2L6EA 3CC7P 1K9MQ 3G21A 2OTLP 1VQ4P 2JYGA 2XT1A 3DPHA 4U0DA 1K8AQ 4GR6A 1QRJA 4XFYA 1QVFO 3DS5A 3DTJA 3G29A 2XV6A 1AUMA 2BUOA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 5DCK A;  4WYM A;  4U0E A;  2M8L A;  4U0A A;  3G0V A;  3H47 A;  3DS0 A;  4PH1 A;  4COP A;  5HGO A;  5I4T G;  4U0C A;  2L6E A;  1A43 A;  1E6J P;  4U0F A;  5HGM A;  4XRO A;  3DS1 A;  1D1D A;  2M8N A;  3G21 A;  3LRY A;  1EOQ A;  4COC A;  1BAJ A;  4XFZ A;  3G28 A;  2M8P A;  2KOD A;  2JYG A;  2XXM A;  2XT1 A;  1A8O A;  4XFX A;  2JO0 A;  3DPH A;  5HGN A;  3H4E A;  4U0D A;  3VRL C;  4PH0 A;  2EIA A;  3MGE A;  3NTE A;  4IPY A;  1EIA A;  5HGL A;  2ONT A;  4QNB A;  2JYL A;  3DS3 A;  3G1I A;  3P05 A;  2XV6 A;  3DS2 A;  4XRQ A;  1QRJ A;  4XFY A;  5JPA A;  3DS4 A;  3DS5 A;  3G26 A;  3DTJ A;  3G29 A;  4U0B A;  2LF4 A;  4M0I A;  1AUM A;  2BUO A;  3G1G A; 
#chains in the Genus database with same CATH topology
 2JBG A;  2M8L A;  3H47 A;  3CCM P;  4COP A;  3CMA P;  2CQ8 A;  2KR5 A;  1AF8 A;  4BPH A;  1VQ8 P;  2KWL A;  2VLP A;  3CC2 P;  2FVE A;  2OTJ P;  2OAR A;  2FAE A;  3CME P;  3EJE A;  3G26 A;  2MR7 A;  2LF4 A;  2N98 A;  3CE7 A;  2LOL A;  1AYI A;  4XRO A;  1D1D A;  2FHS C;  5HVC A;  2KOQ A;  2QEX P;  2KGE A;  3G71 P;  2K2Q A;  1YI2 P;  1QVG O;  1GPJ A;  3HZQ A;  2E1M A;  2LTE A;  5JPA A;  2LML A;  1GXH A;  4BPG A;  3RG2 A;  1VQ7 P;  2GZI A;  4R0M A;  1S72 P;  1VHN A;  5KP7 B;  2PEK A;  1KC8 Q;  1L0I A;  2KGC A;  3P05 A;  3DS2 A;  2QA4 P;  1RNI A;  3EJD A;  2AFD A;  3CXC O;  2L6E A;  2KG9 A;  2L0Q A;  2OTL P;  1VQ4 P;  1NQ4 A;  2K5X A;  2GZG A;  2N50 A;  2VSQ A;  4U0D A;  2FAD A;  1K8A Q;  2JGP A;  1ACP A;  2XZ1 C;  4GR6 A;  1E0H A;  1HQB A;  2XV6 A;  2KOR A;  2PEI A;  2K94 A;  2GDY A;  1YIJ P;  2L4B A;  1K73 Q;  2MR8 A;  1KLP A;  2M8N A;  3G6E P;  1BAJ A;  3CC4 P;  1F80 D;  2JB0 A;  3CPW O;  3CCS P;  2PEO A;  1BXI A;  2KW2 A;  4GR2 A;  4CA3 A;  1DV5 A;  2MY5 A;  1VQN P;  2DGY A;  1YJW P;  5HV8 A;  1KQS O;  1M6N A;  3B4Q A;  5HGM A;  3CCV P;  2K92 A;  2M8P A;  2CWO A;  3I55 P;  4XFX A;  2ROQ A;  4PH0 A;  3VRL C;  2EIA A;  2KG6 A;  2JYL A;  2MF4 A;  4H2X C;  3I56 P;  3G1G A;  2KOO A;  4U0A A;  1NJI Q;  2N6Y A;  5BS1 A;  5HGO A;  3CCU P;  3CCE P;  1VQO P;  2XZ0 D;  3NY7 B;  1M74 A;  2XXM A;  2Z46 A;  1A8O A;  2JO0 A;  2JU1 A;  3Q20 A;  1DNY A;  2ONT A;  2LPK A;  1EMV A;  2AFE A;  2NO8 A;  3G0V A;  2K0X A;  2N5H A;  3GZL A;  3CC7 P;  4UHP B;  4HKG A;  2FQ1 A;  5EJD A;  2AVA A;  3DPH A;  2K0Y A;  2MVU A;  2L9F A;  4XFY A;  1QVF O;  2JAZ A;  2BUO A;  3CCL P;  5BS2 A;  3CCJ P;  2JU2 A;  3OW2 O;  4XFZ A;  3G28 A;  2LL8 A;  2Z45 A;  2GZE A;  2KG8 A;  3HYB A;  1KD1 Q;  4QNB A;  3U43 A;  5KP8 B;  2GYK A;  5F2K A;  5DCK A;  2K0D X;  1ZMB A;  3DS0 A;  2KGA A;  4U0F A;  1E6J P;  1Q82 Q;  1K30 A;  1VKU A;  1VQL P;  4IPY A;  3CCR P;  3M1M A;  2LIU A;  2K93 A;  2KOP A;  2PNG A;  4U0E A;  1VQ6 P;  1YJN P;  1A43 A;  1Q81 Q;  3RG6 C;  3CCQ P;  3LMO A;  1ZNV A;  2EHT A;  4H2Y C;  3NTE A;  1EIA A;  1RO2 A;  1T8K A;  3GJN A;  1RO0 A;  2N6Z A;  2GZF A;  1UJZ A;  4PH1 A;  5F2N A;  5I4T G;  2LIW A;  3GZM A;  2N5I A;  3G21 A;  1HY8 A;  1CEI A;  2JYG A;  2XT1 A;  2GDX A;  1FR2 A;  2ERH A;  1QRJ A;  4NEO A;  1VQ5 P;  1GXG A;  1L0H A;  2FVA A;  2L22 A;  3GKL C;  4U0C A;  3LRY A;  4IZ6 A;  1EOQ A;  3EJB A;  2KOD A;  1OR5 A;  2FAC A;  2EHS A;  3H4E A;  3CD6 P;  2BHV A;  3MGE A;  5KP6 B;  1N8R Q;  4XRQ A;  1M1K Q;  7CEI A;  2M5R A;  3DS4 A;  5F2O A;  4QKO A;  4WYM A;  2PEN A;  2PY8 A;  3G4S P;  1JJ2 O;  2EFJ A;  1YHQ P;  1W2B O;  2AF8 A;  2CG5 B;  1IMQ A;  2PEJ A;  5EW5 E;  1YIT P;  5CZD B;  4MRT C;  1IUQ A;  1MZ8 A;  1M6E X;  5HGL A;  2FQ2 A;  2Z44 A;  1Q86 Q;  4U0B A;  1Q7Y Q;  4BPF A;  2KGD A;  2PEM A;  2P9X A;  2GZJ A;  3WBH A;  1VQ9 P;  3DS1 A;  2LKI A;  4COC A;  4DG9 A;  4F37 A;  1VQK P;  2VLN A;  2EG5 A;  2GDW A;  1VQM P;  1M90 Q;  5HGN A;  2FQ0 A;  1UNK A;  3DS3 A;  4PWV B;  3G1I A;  4PXH B;  1VQP P;  1YJ9 P;  4M0I A;  3E2D A;  2CNR A;  2MD9 A;  3B5I A;  3H0D A;  2PEQ A;  1IMP A;  2KOS A;  2WPT A;  1K9M Q;  1X3O A;  4H2W C;  2DNW A;  2MVV A;  2QNW A;  2VLO A;  2X2B A;  2CGQ A;  2FVF A;  1Z6M A;  3DS5 A;  3DTJ A;  3G29 A;  2VLQ A;  1AUM A;  2JQ4 A; 
#chains in the Genus database with same CATH homology
 2PEI A;  2M8L A;  1VQ5 P;  3H47 A;  3CCM P;  4COP A;  1YIJ P;  4U0C A;  3CMA P;  3CCL P;  5BS2 A;  1K73 Q;  3CCJ P;  3OW2 O;  2M8N A;  3G6E P;  3LRY A;  1EOQ A;  1BAJ A;  4XFZ A;  3CC4 P;  3G28 A;  1VQ8 P;  2KOD A;  3CPW O;  2Z45 A;  3CCS P;  3CC2 P;  2OTJ P;  3H4E A;  3HYB A;  3CD6 P;  2BHV A;  2PEO A;  3MGE A;  1KD1 Q;  2OAR A;  4QNB A;  1N8R Q;  3CME P;  4XRQ A;  1M1K Q;  4GR2 A;  3DS4 A;  3G26 A;  5F2O A;  2LF4 A;  5F2K A;  1VQN P;  5DCK A;  4WYM A;  2DGY A;  1ZMB A;  2PEN A;  2PY8 A;  3DS0 A;  3G4S P;  1JJ2 O;  2EFJ A;  1YHQ P;  1YJW P;  1W2B O;  1KQS O;  1M6N A;  5HGM A;  4U0F A;  1E6J P;  4XRO A;  2PEJ A;  3CCV P;  1YIT P;  1D1D A;  1Q82 Q;  2M8P A;  1K30 A;  1IUQ A;  2QEX P;  2CWO A;  1M6E X;  3I55 P;  4XFX A;  3G71 P;  4PH0 A;  3VRL C;  1VQL P;  1YI2 P;  2EIA A;  4IPY A;  5HGL A;  1QVG O;  3HZQ A;  3CCR P;  3M1M A;  2JYL A;  2E1M A;  2Z44 A;  1Q86 Q;  5JPA A;  4U0B A;  3I56 P;  1Q7Y Q;  3G1G A;  2PEM A;  4U0E A;  4U0A A;  1VQ6 P;  2P9X A;  1NJI Q;  5HGO A;  5BS1 A;  3WBH A;  3CCU P;  1YJN P;  3CCE P;  1A43 A;  1VQO P;  1VQ7 P;  1VQ9 P;  3DS1 A;  1Q81 Q;  3RG6 C;  4COC A;  1S72 P;  3CCQ P;  1VQK P;  2EG5 A;  1M74 A;  1VQM P;  2XXM A;  2Z46 A;  1M90 Q;  2PEK A;  1A8O A;  2JO0 A;  1KC8 Q;  5HGN A;  3Q20 A;  3NTE A;  1EIA A;  2ONT A;  3DS3 A;  3G1I A;  1RO2 A;  3P05 A;  3DS2 A;  1VQP P;  1YJ9 P;  2QA4 P;  1RNI A;  4M0I A;  1RO0 A;  3E2D A;  3G0V A;  4PH1 A;  3B5I A;  5F2N A;  3H0D A;  2PEQ A;  5I4T G;  3CXC O;  2L6E A;  3CC7 P;  1K9M Q;  3G21 A;  2OTL P;  1VQ4 P;  2JYG A;  2XT1 A;  3DPH A;  4U0D A;  1K8A Q;  4GR6 A;  1QRJ A;  4XFY A;  1QVF O;  3DS5 A;  3DTJ A;  3G29 A;  2XV6 A;  1AUM A;  2BUO A; 
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similar chains in the Genus database (?% sequence similarity)
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similar chains in the pdb database (?% sequence similarity)

 
#similar chains in the Genus database (?% sequence similarity)
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#similar chains, but unknotted
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#similar chains in the pdb database (?% sequence similarity)
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