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.

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


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