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
b'MYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPAATLEEMMTACQGVGGPGHKARVL'
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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.

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


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