2KODA

A high-resolution nmr structure of the dimeric c-terminal domain of hiv-1 ca
Total Genus 21
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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
21
sequence length
88
structure length
88
Chain Sequence
MYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPAATLEEMMTACQGVGGPGHKARVL
Loading diagram...

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.

publication title Structural convergence between Cryo-EM and NMR reveals intersubunit interactions critical for HIV-1 capsid function.
pubmed doi rcsb
source organism Hiv-1 m:b_hxb2r
molecule tags Viral protein
molecule keywords HIV-1 CA C-terminal domain
total genus 21
structure length 88
sequence length 88
chains with identical sequence B
ec nomenclature ec 2.7.7.49: RNA-directed DNA polymerase.
pdb deposition date 2009-09-18
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 2kodA00
4M0IA 2M8LA 4PH0A 5DCKA 1A43A 5HGLA 2M8NA 2M8PA 3G29A 4WYMA 2JYGA 5HGOA 1EOQA 3VRLC 3NTEA 1D1DA 2EIAA 1AUMA 3H4EA 3G0VA 4PH1A 4U0CA 3DPHA 2BUOA 2L6EA 1EIAA 1A8OA 2KODA 3DS0A 3LRYA 4COCA 4QNBA 3G28A 2JYLA 3DS4A 5HGMA 5HGNA 3G1GA 1BAJA 3MGEA 4U0FA 2JO0A 3DS1A 4IPYA 3G21A 4U0BA 2XXMA 2XT1A 3H47A 3P05A 3DS3A 4U0DA 4XFXA 3DS5A 4XFZA 4XROA 3G26A 4COPA 2XV6A 4U0AA 2ONTA 4XRQA 1QRJA 4XFYA 5I4TG 1E6JP 2LF4A 3DTJA 5JPAA 4U0EA 3G1IA 3DS2A
chains in the Genus database with same CATH superfamily
2KG8A 2K2QA 3RG2A 3HZQA 2M8PA 2QNWA 2K5XA 1M74A 3CC7P 1VQ7P 2MF4A 2EG5A 2OTLP 4H2XC 3OW2O 1A8OA 2MR8A 2VSQA 3DS4A 1FR2A 3U43A 2CGQA 2MR7A 5HVCA 1YJWP 2PEIA 4F37A 2MVUA 1OR5A 3DS2A 2BHVA 5HGLA 1A43A 1K30A 3EJEA 5BS2A 1AUMA 1UNKA 1YJ9P 4BPFA 2LIWA 2OTJP 2AVAA 1M6NA 2KGDA 5HGMA 1K8AQ 7CEIA 1YJNP 2AFEA 3I55P 2GDYA 5F2NA 1Q82Q 4M0IA 2K92A 2JYGA 3NTEA 1D1DA 1EMVA 2GDXA 2MY5A 4UHPB 2N5HA 3CD6P 2NO8A 2CNRA 4QNBA 2FQ0A 3CCLP 4PXHB 2DGYA 4XFXA 5CZDB 4XRQA 2L22A 5EW5E 1VQ9P 2LKIA 3G6EP 2FVEA 2GZIA 3CCQP 3VRLC 2L4BA 2JB0A 2PEMA 1IUQA 3G0VA 2M5RA 1JJ2O 2GDWA 4COCA 1RO2A 3LRYA 1HQBA 2JU1A 1RNIA 3CCMP 1CEIA 1E0HA 5KP8B 1GXHA 3HYBA 5JPAA 4BPHA 2FVAA 3G1IA 2M8LA 2CG5B 4BPGA 1EOQA 1GXGA 1NJIQ 1Z6MA 2PENA 1VQ8P 1YI2P 5KP6B 3GKLC 1Q86Q 2QA4P 2L6EA 2PEOA 1YIJP 4IZ6A 2L0QA 4U0DA 2JQ4A 2PEQA 4U0AA 2PEKA 2ROQA 3CC2P 4U0EA 2M8NA 1RO0A 2PEJA 1QVGO 1AF8A 2FQ2A 3CMEP 2JBGA 2JU2A 2N98A 2MVVA 4U0BA 2N6YA 3H47A 2N50A 1UJZA 1VQKP 3G26A 3EJBA 1Q81Q 2GZEA 3EJDA 3GZMA 1HY8A 2WPTA 2KOOA 1DNYA 2Z46A 2VLPA 3DPHA 1VQMP 3G28A 2JYLA 3G21A 2GZFA 3DS3A 1YITP 2GZGA 1DV5A 2VLNA 1L0HA 2FHSC 4H2WC 4HKGA 2E1MA 1VQ5P 5DCKA 5HV8A 2VLQA 2K0YA 2LOLA 4U0CA 4DG9A 3NY7B 1T8KA 3GZLA 3WBHA 2PY8A 1MZ8A 1X3OA 4U0FA 2FQ1A 2XT1A 3DS5A 4CA3A 4WYMA 2VLOA 5HGOA 5F2OA 4PH1A 1EIAA 2CWOA 1VQPP 2QEXP 1VQ4P 2GYKA 4H2YC 1VKUA 2PNGA 2XXMA 2DNWA 5F2KA 1L0IA 3G71P 3P05A 2FADA 2N5IA 4QKOA 1NQ4A 2KORA 1K9MQ 2GZJA 3CXCO 5EJDA 1VQ6P 3Q20A 4NEOA 3CCJP 2LMLA 2KOPA 3CE7A 2JAZA 3I56P 2LIUA 1S72P 2KGAA 2KW2A 2AF8A 3CMAP 2L9FA 2BUOA 2N6ZA 4MRTC 4GR2A 3G4SP 3MGEA 3CCEP 2EHTA 2XV6A 3DTJA 2FACA 3LMOA 2XZ1C 2K93A 2K94A 1QVFO 3M1MA 2KGCA 1IMPA 2KOSA 5HGNA 3G1GA 1BAJA 2KR5A 2LPKA 1KC8Q 1YHQP 2ONTA 2KG9A 2Z45A 1E6JP 2LF4A 3CC4P 2XZ0D 1VQOP 2KGEA 2EFJA 3B4QA 2EHSA 2K0DX 1VQNP 3H0DA 2KODA 2K0XA 4IPYA 3CCUP 1GPJA 1QRJA 4XFYA 2OARA 3E2DA 1K73Q 1KD1Q 2KWLA 2LTEA 1M1KQ 2CQ8A 2JGPA 4PWVB 3GJNA 4COPA 1N8RQ 1F80D 4PH0A 3G29A 1IMQA 1VQLP 1M90Q 3B5IA 1Q7YQ 2FVFA 1AYIA 1W2BO 5KP7B 1KQSO 2P9XA 1ZMBA 1ZNVA 3CCSP 2X2BA 2FAEA 4GR6A 2EIAA 2KOQA 2ERHA 2Z44A 3CPWO 3CCRP 2MD9A 2AFDA 1VHNA 3DS0A 5BS1A 1ACPA 2KG6A 3CCVP 2LL8A 2JO0A 3DS1A 1M6EX 4XROA 4R0MA 1KLPA 4XFZA 3RG6C 5I4TG 3H4EA 1BXIA
chains in the Genus database with same CATH topology
2M8LA 3HZQA 2M8PA 3CC4P 4WYMA 1VQOP 5HGOA 1EOQA 1M74A 3CC7P 1VQ7P 2EFJA 1NJIQ 2PENA 1VQ8P 5F2OA 2EG5A 1YI2P 4PH1A 1Q86Q 2QA4P 2OTLP 1VQNP 3OW2O 3H0DA 2CWOA 1EIAA 1A8OA 2KODA 2L6EA 2PEOA 1YIJP 3DS4A 1VQPP 2QEXP 1VQ4P 4IPYA 2XXMA 3CCUP 4U0DA 5F2KA 2PEQA 4U0AA 1YJWP 2PEIA 1QRJA 4XFYA 2PEKA 2OARA 3G71P 3CC2P 4U0EA 3P05A 2BHVA 3DS2A 3E2DA 5HGLA 1A43A 2M8NA 1K30A 1K73Q 5BS2A 1K9MQ 1AUMA 1YJ9P 1RO0A 2PEJA 1QVGO 2OTJP 3CXCO 1KD1Q 3CMEP 1M6NA 1VQ6P 5HGMA 3Q20A 1M1KQ 1K8AQ 3CCJP 4U0BA 3H47A 1YJNP 1VQKP 3G26A 4COPA 3I56P 3I55P 1N8RQ 5F2NA 1Q82Q 1Q81Q 4M0IA 4PH0A 1S72P 3G29A 2JYGA 3NTEA 1VQLP 1M90Q 1D1DA 3B5IA 2Z46A 3CMAP 3DPHA 2BUOA 1Q7YQ 3CD6P 1VQMP 4GR2A 4QNBA 3G28A 2JYLA 3G4SP 1W2BO 3CCLP 3MGEA 5I4TG 3CCEP 2DGYA 3G21A 4XFXA 3DS3A 1YITP 1KQSO 2P9XA 1ZMBA 2XV6A 4XRQA 3CCSP 3DTJA 2E1MA 1VQ5P 1VQ9P 5DCKA 4GR6A 3G6EP 3CCQP 3VRLC 2EIAA 1QVFO 2Z44A 3CPWO 2PEMA 1IUQA 3G0VA 3CCRP 4U0CA 1JJ2O 3M1MA 3DS0A 1RO2A 3LRYA 4COCA 5BS1A 3WBHA 2PY8A 5HGNA 3G1GA 1BAJA 4U0FA 3CCVP 2JO0A 3DS1A 1KC8Q 1YHQP 1RNIA 3CCMP 2XT1A 1M6EX 4XROA 3DS5A 4XFZA 3RG6C 3HYBA 2ONTA 5JPAA 2Z45A 1E6JP 2LF4A 3H4EA 3G1IA
chains in the Genus database with same CATH homology


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